Last data update: 2014.03.03
R: Bicluster Membership Graph
biclustmember R Documentation
Bicluster Membership Graph
Description
Draws a membership graph cluster x columns
Usage
biclustmember(bicResult, x, mid = T, cl_label = "", which=NA,
main = "BiCluster Membership Graph", xlab="Cluster",
color=diverge_hcl(101, h = c(0, 130)), ...)
clustmember(res, x, mid = T, cl_label = "", which=NA,
main = "Cluster Membership Graph", xlab="Cluster",
color=diverge_hcl(101, h = c(0, 130)), ...)
bicorder(bicResult, cols=TRUE, rev=FALSE)
Arguments
x
The data matrix
bicResult
BiclustResult object with a bicluster result set.
res
Cluster Result (is converted into a kcca object)
mid
If TRUE, shows the value of the remaining objects inside the cluster value, else shows both aside each other.
cl_label
Ticks of x-axis
which
If specified gives the ploting order of the columns from bottom to top
main
Gives the title of the plot
xlab
Label of x-axis
color
Range of colors for the plot
...
Additional plot options or if neccessary option for as.kcca
cols
If TRUE orders the column by appearance in the bicluster, else orders the rows.
rev
If TRUE reverses the order
Author(s)
Sebastian Kaiser
sebastian.kaiser@stat.uni-muenchen.de
See Also
bubbleplot
for simultaneous representation of biclusters,
parallelCoordinates
for single representation of biclusters as lines of gene or condition profiles,
drawHeatmap
for Heatmap representation of biclusters and
biclustbarchart
for a barchart.
Examples
set.seed(1)
x=matrix(rnorm(900),30,30)
x[1:5,1:5]=rnorm(25,3,0.3)
x[11:15,11:15]=rnorm(25,-3,0.3)
x[21:25,21:25]=rnorm(25,6,0.3)
colnames(x)<-paste("Var.",1:30)
bics <- biclust(x,BCPlaid(), back.fit = 2, shuffle = 3, fit.model = ~m + a + b,
iter.startup = 5, iter.layer = 30, verbose = TRUE)
biclustmember(bics,x)
ord<-bicorder(bics, cols=TRUE, rev=TRUE)
biclustmember(bics,x,which=ord)
Results